Genomic and phenotypic characterization of Rhizobium gallicum phage vB_RglS_P106B

Abstract

The phage P106B (vB_RglS_P106B) is a Siphoviridae phage with a narrow spectrum of infectivity, which has been isolated from soils with a history of pea cultivation. The trapping host of P106B is an indigenous strain of Rhizobium gallicum (SO14B-4) isolated from soils associated with Vicia cracca. Phenotypic characterization of the phage revealed that P106B has an approximate burst size of 21 p.f.u. per infected cell with 60 min and 100 min eclipse and latent periods, respectively. Phage P106B was unable to transduce under the conditions tested. The genome of P106B is 56 024 bp in length with a mean DNA G+C content of 47.9 %. The complete genome sequence contains 95 putative ORFs and a single tRNA gene coding for leucine with the anticodon TTA. Putative functions could only be assigned to 22 of the predicted ORFs while a significant number of ORFs (47) shared no sequence similarities to previously characterized proteins. The remaining 26 putative protein-coding genes exhibited a sequence resemblance to other hypothetical proteins. No lysogeny-related genes were found in the P106B genome.

Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

“…When only one or a handful of affiliated isolate genomes were included in the VC and lacked genus-level classification, a candidate name was derived from the isolate (if several isolates, from the first one isolated). This was the case for VC_5 (Cbaphi381virus 67 ), VC_12 (P12024virus 68 ), VC_14 (MED4-117virus), VC_19 (HMO-2011virus 69 ), VC_31 (RM378virus 70 ), VC_36 (GBK2virus 71 ), VC_47 (Cbaphi142virus 67 ) , and VC_277 (vB_RglS_P106Bvirus 72 ). Otherwise, VCs were considered as "new VCs".…”

A bacteriophage infectingMesorhizobiumspecies has a prolate capsid and shows similarities to a family ofCaulobacter crescentusphages

“…M. japonicum strain R7A was used as the trapping host. The procedure followed in the isolation is as described in Halmillawewa et al (2015) which was a modified version of the previously described method of Mendum et al (2001) that incorporated an enrichment step consisting of incubating the soil sample in an exponentially growing culture of the trapping strain. Isolated phages were detected by standard plaque assays as described by Adams (1959).…”

“…Of these rhizobiophages, only one is a Mesorhizobium phage: Lo5R7ANS (Genbank accession: KM199771) (Halmillawewa 2014). All the others are phages isolated by using Rhizobium or Sinorhizobium species as trapping hosts (for example see papers by Schulmeister et al 2001;Deák et al 2010;Restrepo 2012;Engelhardt et al 2013;Brewer et al 2014Brewer et al , 2018Santamaría et al 2014;Dziewit et al 2014;Halmillawewa 2014;Halmillawewa et al 2015Halmillawewa et al , 2016Schouten et al 2015;Crockett et al 2015;Johnson et al 2015Johnson et al , 2017Fleagle et al 2018;Cubo et al 2020;Gunathilake et al 2020).…”

Complete Genome Sequence of Sinorhizobium Phage ΦM6, the First Terrestrial Phage of a Marine Phage Group

“…Data are limited on the diversity of bacteriophages that prey upon nitrogen-fixing soil bacteria, which are among the most important microbes in agriculture. Our lack of knowledge of rhizobial phages also limits our understanding of the effects of phage predation on rhizobial survival both in soil and in crop bioinoculants ( 2 – 4 ). ΦM6 is a bacteriophage from a historical collection ( 2 ) and infects Sinorhizobium meliloti SU47, a nitrogen-fixing symbiont of Medicago truncatula (barrel medic), and Medicago sativa (alfalfa) ( 5 , 6 ).…”